The Joker was trying to make an analogy. He was saying that he lacks belief in our intelligence the same way we lack belief in God's intelligence, and he was waiting for evidence. He thought that that made us look silly for waiting for evidence of God's intelligence because his obtusely ignoring evidence of our intelligence was indeed silly.
The problem is, of course, that it's a completely false analogy.
The problem is, of course, that it's a completely false analogy.